You may have a scratch or something on the disc that is just in the right spot to mess up that bit of data. Check the underside and maybe give it a cleaning with a soft cloth wiping from the center outwards.

Yeah the bottom of the disc maybe scratched or just dirty try to clean it. Chrono Cross is a great game so I hope you get it fixed. I was actually thinking the other day that I wish I still had it so I could play it again. Well good luck buddy!